Imaging techniques for measuring lung ventilation are essential tools to study lung tissue response to radiation therapy. Most of the existing CT and image registration based ventilation measurement methods use two extreme phases (end expiration and end inspiration) while ignoring the important ventilation variation within the respiratory cycle. In this paper, we present a new instantaneous ventilation measurement scheme using multiple 4DCT phase images and regularized 3D image registration, which aims at measuring the regional ventilation within the respiratory cycle. The ventilation is measured using the Jacobian (a function of local partial derivatives) of the registration displacement field. For all four animals, 39% of the total lung volume reaches maximum ventilation at T2 (50% inspiration phase) during inspiration and the 75% of the total lung volume reaches maximum ventilation at T 5 (75% expiration phase) during expiration. The registration accuracy assessed by 200 semi-automatically matched landmarks in all phases and animals show landmark error on the order of 1 mm after registration.